Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Find_primer_sequence_and_reverse_complement_read_within_amplicon.fastq script needed

    Hi,

    I have a fastq file with merged amplicon sequence reads post Illumina sequencing. However, the library was build by ligating the Illumina adapters to the amplicon. Therefore, the merged amplicon sequences have no common direction. Now I had the idea to use a script that finds the exact sequence of a certain primer and reverse complements those sequence reads within the fastq file. One _is_ able to do this in Geneious, however, I'd rather like to use a script/tool to incorporate into the pipeline I want to establish.
    I already looked into BBtools and others, however, couldn't find a tool doing this.

    Thank you for any input.

    Cheers,

    Karsten

  • #2
    For reference cross-posted: https://www.biostars.org/p/292377/

    Copying my comment there below.

    Just that part of the sequence or the whole sequence? If whole sequence is fine then you should be able to select matching reads that contain the sequence you are interested in using bbduk.sh and then you can reverse-complement them using reformat.sh.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Current Approaches to Protein Sequencing
      by seqadmin


      Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
      04-04-2024, 04:25 PM
    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 12:08 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 10:19 PM
    0 responses
    14 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 09:21 AM
    0 responses
    14 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-04-2024, 09:00 AM
    0 responses
    43 views
    0 likes
    Last Post seqadmin  
    Working...
    X